Changing geometry in linked duplicates
Let say the object A has a lot of linked duplications, and object A has a mesh called A'. Let say you have a B object with a mesh called B'. You want B' to be part of A. If you select B object, then select A, then ctrlJ, the A object is now made of the A' + B'. All the A linked copies are now made of A' + B'. It won't explode any memory as a linked duplication doesn't weigh on the file.

Now, if B was also linked duplicated and you need to delete all the now useless copies of B (considering B' is now part of A), you can select one of the B objects and press shift L Select Linked > Object Data and it will select all the Bs. Then X to delete.

Does it answer?